Diagenode

ATAC-seq kit

Catalog Number
Format
Price
C01080002
24 rxns
$1,745.00
Other format


ATAC-seq, Assay for Transposase-Accessible Chromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the transposase Tn5 which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:

  •  Gain insight into gene regulation and understand open chromatin signatures
  •  Determine nucleosome positions at single nucleotide resolution
  •  Uncover transcription factor (TF) occupancy

Diagenode’s ATAC-seq kit is based on a highly validated protocol optimized for 50,000 cells per reaction. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.

ATAC-seq kit features:

  • Cell requirement: 50,000 cells / rxn
  • Robust protocol with high reproducibility between replicates and repetitive experiments
  • Easy and efficient DNA capture after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)
  • Additional qPCR step to determine the number of cycles needed for library amplification:  
    • Avoids over-amplification
    • Allows adaptation/flexibility for more challenging samples to succeed with library prep.
    • Gives early indication if the experiment does not work (no qPCR amplification)

Looking for ATAC-seq on tissue? Please, go to: ATAC-seq package for tissue

  • Method overview

    ATAC-seq, Assay for Transposase-Accessible Chromatin, followed by next generation sequencing, is a key technology to easily identify the open regions of the chromatin. The protocol consists of 3 steps: nuclei preparation, tagmentation and library amplification. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which  cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.

    ATAC-seq kit workflow

  • Example of results

    library prepared with the Diagenode ATAC-seq kit

    Figure 1.Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.

    Diagenode ATAC-seq kit

    Figure 2. Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)

    Assay for Transposase-Accessible Chromatin

    Assay for Transposase-Accessible Chromatin

    Figure 3 Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.

     open chromatin regions

    Figure 4.
    Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.

  • Additional solutions for ATAC-seq kit
  •  Documents
    ATAC-seq Kit - Manual MANUAL
    Gene expression is carefully regulated in the cells in order to manage a wide range of biological...
    Download
    Chromatin Brochure BROCHURE
    Whether you are experienced or new to the field of chromatin immunoprecipitation, Diagenode has e...
    Download
  •  Safety sheets
    ATAC-seq kit SDS GB en Download
    ATAC-seq kit SDS US en Download
    ATAC-seq kit SDS BE nl Download
    ATAC-seq kit SDS BE fr Download
    ATAC-seq kit SDS FR fr Download
    ATAC-seq kit SDS ES es Download
    ATAC-seq kit SDS DE de Download
    ATAC-seq kit SDS JP ja Download
  •  Publications

    How to properly cite this product in your work

    Diagenode strongly recommends using this: ATAC-seq kit (Diagenode Cat# C01080002). Click here to copy to clipboard.

    Using our products in your publication? Let us know!

    Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches
    Lee M. et al.
    Transcriptional regulation controls cellular functions through interactions between transcription factors (TFs) and their chromosomal targets. However, understanding the fate conversion potential of multiple TFs in an inducible manner remains limited. Here, we introduce iTF-seq as a method for identifying individual...

    Protocol to isolate nuclei from Chlamydomonas reinhardtii for ATAC sequencing
    Santhanagopalan I. et al.
    Highlights Optimized isolation of nuclei from the green model alga Chlamydomonas reinhardtii Tag-free isolation from both cell-walled and cell wall-deficient algae strains Key steps for an effective and fast isolation and quantification procedure of nuclei Extracts at a quality suitabl...

    Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition
    Trembley B.J.M. et al.
    Translation of seed stored mRNAs is essential to trigger germination. However, when RNAPII re-engages RNA synthesis during the seed-to-seedling transition has remained in question. Combining csRNA-seq, ATAC-seq and smFISH in Arabidopsis thaliana we demonstrate that active transcription initiation is detect...

    The transcriptional regulatory network modulating human trophoblast stem cells to extravillous trophoblast differentiation
    Kim M. et al.
    During human pregnancy, extravillous trophoblasts play crucial roles in placental invasion into the maternal decidua and spiral artery remodeling. However, regulatory factors and their action mechanisms modulating human extravillous trophoblast specification have been unknown. By analyzing dynamic changes in transcr...

    DMSO derives Trophectoderm and Clonal Blastoid from Single Human Pluripotent Stem Cell
    Alsolami S. et al.
    Human naïve pluripotent stem cells (nPSCs) can differentiate into extra-embryonic trophectoderm (TE), a critical step in the generation of the integrated embryo model termed blastoid. The current paradigm of blastoid generation necessitates the aggregation of dozens of nPSCs treated with multiple small molecule...

    In vitro production of cat-restricted Toxoplasma pre-sexual stages
    Antunes, A.V. et al.
    Sexual reproduction of Toxoplasma gondii, confined to the felid gut, remains largely uncharted owing to ethical concerns regarding the use of cats as model organisms. Chromatin modifiers dictate the developmental fate of the parasite during its multistage life cycle, but their targeting to stage-specific cistro...

    Inflammatory stress-mediated chromatin changes underlie dysfunction in endothelial cells
    Liu H. et al.
    Inflammatory stresses underlie endothelial dysfunction and contribute to the development of chronic cardiovascular disorders such as atherosclerosis and vascular fibrosis. The initial transcriptional response of endothelial cells to pro-inflammatory cytokines such as TNF-alpha is well established. However, very few ...

    Dynamic PRC1-CBX8 stabilizes a porous structure of chromatin condensates
    Uckelmann M. et al.
    The compaction of chromatin is a prevalent paradigm in gene repression. Chromatin compaction is commonly thought to repress transcription by restricting chromatin accessibility. However, the spatial organisation and dynamics of chromatin compacted by gene-repressing factors are unknown. Using cryo-electron tomograph...

    UMSBP2 is chromatin remodeler that functions in regulation of geneexpression and suppression of antigenic variation in trypanosomes.
    Soni A. et al.
    Universal Minicircle Sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind the single-stranded G-rich UMS sequence, conserved at the replication origins of minicircles in the kinetoplast DNA, the mitochondrial genome of kinetoplastids. Trypanosoma brucei UMSBP2 has been recently shown to co...

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